Hi All, I have gene expression data with ENSEMBL Ids (ENSG00000XXXXXXX). I tried 3 different packages to convert them to ENTREZ IDs (bitr, biomatRt, AnnotationDb), but I consistently get no match for about 5-6% of the genes. I would like to do GO and GSEA, but most GO and GSEA tools require gene symbols or entrez IDs. This problem bugs me for a while already. How to handle this? I work with mouse genes.
Here are the example of what I am doing:
MyTargetList$entrez <- mapIds(org.Mm.eg.db,
keys=rownames(IP_toptreatRT3),
column ="ENTREZID",
keytype="ENSEMBL",
multiVals="first")
Or with biomaRt:
ensembl = useMart(biomart = "ensembl", dataset = "mmusculus_gene_ensembl")
genemap <- getBM( attributes = c("ensembl_gene_id", "entrezgene"),
mart = ensembl )
and then match function to populate the column.
But there seem to be gaps in the databases:
> head(genemap)
ensembl_gene_id entrezgene
1 ENSMUSG00000064336 NA
2 ENSMUSG00000064337 NA
3 ENSMUSG00000064338 NA
4 ENSMUSG00000064339 NA
5 ENSMUSG00000064340 NA
6 ENSMUSG00000064341 17716
Cheers, Lech
•
written
by
lech.kaczmarczyk •
1 answer
It might help to retrieve HGNC names:
#!/usr/bin/env python
import sys
from mygene import MyGeneInfo
mg = MyGeneInfo()
genes = ["ENSMUSG00000064336",
"ENSMUSG00000064337",
"ENSMUSG00000064338",
"ENSMUSG00000064339",
"ENSMUSG00000064340",
"ENSMUSG00000064341"]
sys.stdout.write("%s\t%s\t%s\n" % ("ensembl", "hgnc", "entrezgene"))
for gene in genes:
result = mg.query(gene, fields=["symbol", "entrezgene"], species="mouse", verbose=False)
for hit in result['hits']:
if 'symbol' not in hit:
hit['symbol'] = "NA"
if 'entrezgene' not in hit:
hit['entrezgene'] = "NA"
sys.stdout.write("%s\t%s\t%s\n" % (gene, hit['symbol'], hit['entrezgene']))
Sample run:
$ ./convert_records.py
ensembl hgnc entrezgene
ENSMUSG00000064336 mt-Tf NA
ENSMUSG00000064337 mt-Rnr1 NA
ENSMUSG00000064338 mt-Tv NA
ENSMUSG00000064339 mt-Rnr2 NA
ENSMUSG00000064340 mt-Tl1 NA
ENSMUSG00000064341 ND1 17716
Looking at HGNC names in GeneCards or other resources, for example, may help with searching for Entrez Gene records that may not be available directly through these sources.
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It's probably useful if you add a few examples for which you can't find a match for us to replicate your issue.
In addition, showing, the code you used in one of those packages could allow us to spot a mistake.
Hi, thanks for quick reply. I did add the examples. Since I get most of the records, I would assume it's just missing records in the database (see NAs after retriving biomaRt annotations).
Most of the NAs are mitochondrial genes.
All of them are non-protein-coding.
not all as it seems:
.................
There's no way to map all Ensembl IDs to Entrez Gene IDs, the latter is a much smaller dataset than the former.